Green Party leader John Gormley and Justice Minister Dermot Ahern have already dismissed claims from the bishops that the Civil Partnership Bill may be unconstitutional.
The Catholic Church has already called for TDs to be allowed a free vote on the issue.
Mr Ahern is to bring the legislation, which stops short of full gay marriage, before the Dail next month but it could be the autumn before it becomes law. It sets out a legal safety net on rights for same-sex couples living in long-term relationships.
"That legislation is part of the Programme for Government and will be implemented," Mr Cowen said yesterday.
He added: "It will be enacted and we're doing so on the basis of careful advice from the Attorney General, which is consistent with the Constitution. We're looking forward to implementing it as soon as possible."
In a statement following their summer conference in May- nooth, the bishops called on the Government to introduce amendments to the bill to accommodate freedom of religious conscience.
The bill, if passed in its present form, would impose a fine and/or imprisonment on registrars who refused to carry out a same-sex union on religious grounds. The registrar could also be sacked.
SIC: II